Apple's new high-speed Thunderbolt technology is still in its infancy, and as a result its initial implementations have had a few minor bugs and performance issues. Apple has released a firmware update to address some bugs relating to the new I/O technology.
The firmware update should be available via Software Update for these systems, but can also be downloaded from the Thunderbolt Firmware Update Web site and applied manually; it is a small download of approximately 500KB. Even though the update's Web site shows a picture of a MacBook Pro, the update is for all systems that have Thunderbolt connections.
When installed, the firmware update will require you to restart your system and will then show a gray screen with a progress bar. Be sure you do not interrupt this process at all, and keep your computer attached to a reliable wall power outlet. The update may reboot a couple of times, and then should boot normally once complete.
After restarting, the system may take slightly longer than usual to load initially, since the system may detect the Thunderbolt update as new hardware to configure, and thereby have to update boot caches and other system resources. If this is the case, then subsequent reboots should be faster again.